Objectives: Nocardia, a Gram-positive bacterium, is responsible for rare and severe infections. Accurate microbiological data are essential to guide antibiotic treatment. Our primary objective was to describe species identification and results of antimicrobial susceptibility testing (AST) for Nocardia isolates analysed over a 6-year period. Secondary objectives were to study temporal trends in species distribution and AST results. Methods: We retrospectively analysed results from Nocardia isolates sent between January 2010 and December 2015 to a French laboratory dedicated to Nocardia (Observatoire Francais des Nocardioses). Species identification was obtained by amplification and sequencing of a 600-bp fragment of the 16S rRNA gene (for all isolates) and of hsp65 (when required). AST was performed using disk diffusion. Results: We included 793 Nocardia isolates, mostly from the lungs (53.8%). The most frequent species were Nocardia farcinica (20.2%), Nocardia abscessus complex (19.9%) and Nocardia nova complex (19.5%). The proportion of N. farcinica increased significantly over time from 13% in 2010 to 27.6% in 2014. Linezolid, amikacin, trimethoprim-sulfamethoxazole, minocycline and imipenem were the most frequently identified active antibiotics with, respectively, 0% (0/734), 2.9% (21/730), 5.4% (40/734), 9.4% (69/734) and 19.5% (143/732) of isolates not susceptible. Nocardia farcinica was frequently not susceptible to cefotaxime (118/148, 79.7% of the isolates), but only about 5% of Nocardia cyriacigeorgica and N. abscessus complex isolates were not susceptible to cefotaxime. Conclusions: In this first epidemiological study of Nocardia isolated from human samples in France, N. farcinica was the species most frequently identified and its prevalence increased over time. (C) 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Les Nocardia sont des bactéries à Gram positif responsables de pathologies rares mais graves. Disposer de données microbiologiques précises (sensibilité aux antibiotiques et typage moléculaire d’espèce) sur un grand nombre de souches est indispensable afin de choisir le traitement probabiliste puis de l’adapter. Notre objectif principal était de décrire la sensibilité aux antibiotiques et l’épidémiologie moléculaire des Nocardia en France sur une large collection de souches. Notre objectif secondaire était d’étudier l’évolution au cours du temps de la résistance aux antibiotiques et de la proportion de chaque espèce et d’évaluer la répartition géographique des souches collectées. Nous avons analysé rétrospectivement les données relatives aux souches de Nocardia isolées chez l’homme durant 6 ans (2010–2015). L’identification d’espèce était obtenue par amplification et séquençage d’un fragment de 600pb du gène codant pour l’ARNr 16S (pour toutes les souches) et le gène hsp65 (pour les complexes N . abscessus et N . transvalensis ). La sensibilité aux antibiotiques était évaluée par technique de diffusion des antibiotiques en disques sur gélose Mueller-Hinton ajustée en cations. Nous avons inclus 793 souches de Nocardia , principalement isolées au niveau pulmonaire (53,8 %) ou à partir de lésions cutanées ou sous-cutanées (19,7 %). Les principales espèces étaient N . farcinica (20,2 %), N . abscessus complexe (19,9 %), N . nova complexe (19,5 %) et N . cyriacigeorgica (12,9 %). La proportion de N . farcinica augmentait significativement au cours du temps. Le linézolid, l’amikacine, le triméthoprime-sulfaméthoxazole, la minocycline, et l’imipénem étaient les antibiotiques les plus souvent actifs in vitro avec respectivement 0 %, 2,9 %, 7 %, 9,4 %, 13,8 % et 19,5 % de souches non sensibles ; ces fréquences étaient stables au cours du temps. N . farcinica était souvent non sensible aux céphalosporines de 3 e génération (∼ 80 % des souches), mais seulement 5 % des N . cyriacigeorgica et des N . abscessus complexe n’étaient pas sensibles au céfotaxime et à la ceftriaxone. Une plus grande densité de souches était observée dans le Sud-Est de la France et dans les territoires d’Outre-Mer, par rapport au Nord de la France. Dans cette première étude épidémiologique des souches de Nocardia isolées chez l’Homme en France, N . farcinica était la principale espèce identifiée et sa proportion augmentait au cours du temps.

This study aims at genetic characterization and phylogenetic relationships of Nocardia brasiliensis focusing by using housekeeping rrs, hsp65, and sodA genes. N. brasiliensis is the species responsible for 80% of cases of actinomycetoma, one form of cutaneous nocardiosis which occurs mainly in tropical regions reaching immunocompetent patients in which the disease can lead to amputation. We analyze 36 indigenous cases of N. brasiliensis that happened in France. Phylogenetic analysis targeting rrs gene showed no robustness at phylogenetic nodes level. However, the use of a concatenation of hsp65 and sodA genes showed that the tested strains surprisingly ranked in 3 well-defined genotypes. Genotypes 2 and 3 were phylogenetically closer to each other and both diverged from genotype 1 sustained by a high bootstrap of 81%. This last genotype hosts all the cases of pulmonary forms (3), the sole cerebral form, and almost all the cases of immunocompromised patients (3 out of 4). Moreover, excepting one of them, all the strains belonging to this group present a susceptibility to imipenem which is not the case in the other genotypes that rarely count among them strains being susceptible to this drug. The haplotype diversity (Hd) of hsp65 (0.927) and sodA (0.885) genes was higher than that of rrs (0.824). For this gene, we obtained 16 polymorphic sites whereas, for hsp65 and sodA genes, up to 27 and 29 were identified, respectively. This study reveals that these two genes have an important genetic discriminatory power for the evaluation of the intraspecies genetic variability of N. brasiliensis and they may be useful for identification purposes at species level. This study also reveals the possible existence of a new species harbored by genotype 1.

Currently for bacterial identification and classification the rrs gene encoding 16S rRNA is used as a reference method for the analysis of strains of the genus Nocardia. However, it does not have enough polymorphism to differentiate them at the species level. This fact makes it necessary to search for molecular targets that can provide better identification. The sodA gene (encoding the enzyme superoxide dismutase) has had good results in identifying species of other Actinomycetes. In this study the sodA gene is proposed for the identification and differentiation at the species level of the genus Nocardia. We used 41 type species of various collections; a 386 bp fragment of the sodA gene was amplified and sequenced, and a phylogenetic analysis was performed comparing the genes rrs (1171 bp), hsp65 (401 bp), secA1 (494 bp), gyrB (1195 bp) and rpoB (401 bp). The sequences were aligned using the Clustal X program. Evolutionary trees according to the neighbour-joining method were created with the programs Phylo_win and MEGA 6. The specific variability of the sodA genus of the genus Nocardia was analysed. A high phylogenetic resolution, significant genetic variability, and specificity and reliability were observed for the differentiation of the isolates at the species level. The polymorphism observed in the sodA gene sequence contains variable regions that allow the discrimination of closely related Nocardia species. The clear specificity, despite its small size, proves to be of great advantage for use in taxonomic studies and clinical diagnosis of the genus Nocardia.

Some bacterial species recovered from the airways of cystic fibrosis (CF) patients are indisputably associated with lung infections, whereas the clinical relevance of others, such as Nocardia spp., remains unclear. Sixteen French CF cases of colonization/infection with Nocardia spp. were reviewed in order to evaluate the epidemiology, the clinical impact and the potential treatment of these bacteria, and results were compared to those of the literature. Five Nocardia species were identified, Nocardia cyriacigeorgica being the major species (50 % of cases). At first isolation, Nocardia was the sole pathogen recovered in six patients. Seven patients presented pulmonary exacerbation. For 12 patients, antimicrobial treatment against Nocardia was started immediately, mainly based on cotrimoxazole (6 of the 12 cases). In this study, we highlight the heterogeneity of the clinical management of Nocardia spp. in CF. Guidelines for the clinical management of Nocardia infections in CF patients are proposed.

Introduction: Nocardiosis emerges as a serious infection in the immunocompromised patient, causing an aggressive clinical picture, which requires prolonged treatment. Case presentation: We present five cases of disseminated nocardiosis in patients under corticosteroid therapy with four different forms of clinical presentation. Conclusion: Immunocompromised patients are at increased risk of disseminated nocardiosis, which may require extended culture time for diagnosis and molecular methods. The cases emphasize the relevance of a careful evaluation of the central nervous system, a common target in nocardiosis dissemination.

Background Nocardia cyriacigeorgica is recognized as one of the most prevalent etiological agents of human nocardiosis. Human exposure to these Actinobacteria stems from direct contact with contaminated environmental matrices. The full genome sequence of N. cyriacigeorgica strain GUH-2 was studied to infer major trends in its evolution, including the acquisition of novel genetic elements that could explain its ability to thrive in multiple habitats. Results N. cyriacigeorgica strain GUH-2 genome size is 6.19 Mb-long, 82.7% of its CDS have homologs in at least another actinobacterial genome, and 74.5% of these are found in N. farcinica . Among N. cyriacigeorgica specific CDS, some are likely implicated in niche specialization such as those involved in denitrification and RuBisCO production, and are found in regions of genomic plasticity (RGP). Overall, 22 RGP were identified in this genome, representing 11.4% of its content. Some of these RGP encode a recombinase and IS elements which are indicative of genomic instability. CDS playing part in virulence were identified in this genome such as those involved in mammalian cell entry or encoding a superoxide dismutase. CDS encoding non ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) were identified, with some being likely involved in the synthesis of siderophores and toxins. COG analyses showed this genome to have an organization similar to environmental Actinobacteria. Conclusion N. cyriacigeorgica GUH-2 genome shows features suggesting a diversification from an ancestral saprophytic state. GUH-2 ability at acquiring foreign DNA was found significant and to have led to functional changes likely beneficial for its environmental cycle and opportunistic colonization of a human host.

Nocardia spp. are bacteria often implicated in pulmonary diseases and central nervous system infections, especially in immunocompromised patients. We report here the case of an immunocompromised woman presenting an insidious brain abcess initially treated as a cerebral stroke. Despite a cotrimoxazole and rifampicin treatment she did not improve. She died 3 month later after she stopped her treatment.

Commercial dried food emulsions, with high fat content (50 g fat 1100 g), were prepared at plant scale from whey and palm oil. Five powders were analyzed: powder without fines, taken from the bottom of the spray-dryer chamber; fines 1 and fines 2 respectively collected at the bottom of the first and second cyclones, a mix of fines 1 and fines 2 and the final powder, taken during packing. Scanning electronic and optical microscopy showed only spherical particles and also indicated that fines 2 were roughly twice as smaller as other powder particles. Free fat content was significantly higher in fines than in final powder. Reconstituted emulsions (10 g powder/100 g water) were analyzed by laser light scattering. Aggregation and coalescence indexes were very low, except in reconstituted emulsions made with fines 2. This is consistent with their high free fat content and suggests that this results from processing through the cyclones. (C) 2013 Elsevier Ltd. All rights reserved.

We report the first case of cerebral abscess due to a novel species of Nocardia in a heart transplant patient and describe the antimicrobial susceptibility of this isolate. As our patient was intolerant to trimethoprim-sulfamethoxazole, we also discuss alternative therapeutic options in brain abscess due to Nocardia sp.

The pathogenic strain Nocardia cyriacigeorgica GUH-2 was isolated from a fatal human nocardiosis case, and its genome was sequenced. The complete genomic sequence of this strain contains 6,194,645 bp, an average G+C content of 68.37%, and no plasmids. We also identified several protein-coding genes to which N. cyriacigeorgica's virulence can potentially be attributed.

Background. - Mexico has the largest number of clinical cases of actinomycetoma in North and South America. Species originally identified by less specific methods have been recently reclassified as other known species or as new species.Objective. - To assess, by 16S rRNA gene sequencing and phenotypic methods, the species distribution of 18 human clinical isolates originally identified as N. brasiliensis, some of them isolated between 1947 and 1959 in Mexico City.Methods. - Clinical isolates came from the Hospital General, "Dr. Manuel Gea Gonzalez", and Instituto Nacional de Diagnostic y Referencia Epidemiologica (INDRE) in Mexico, D.F. The strains used in this study included 15 clinical strains isolated between 1947 and 1959 that were originally identified as N. brasiliensis and three more strains obtained in 2007 identified as Nocardia spp. The isolates were identified genotypically by sequencing the 165 rRNA gene, and their phenotypic profiles were obtained with the API Coryne (R) system. Antibiotic susceptibility patterns were tested according to the protocol of the Comite de l'antibiogramme de la Societe francaise de microbiologie [4].Results. - According to 165 rRNA gene, sequencing were identified among 18 human clinical isolates as Nocardia farcinica (n = 11) and Nocardia brasiliensis (n = 7). A high number of the strains were susceptible to the majority of the antibiotics tested. The phenotypic profiles of the strains were quite uniform for N. farcinica and some variability was observed for N. brasiliensis strains.Conclusion. - N. farcinica was the most prevalent species identified. Modern methodologies should be applied in clinical laboratories to accurately identify etiological agents. (C) 2011 Elsevier Masson SAS. All rights reserved.

ABSTRACT Nocardia spp. can lead to local or disseminated infections, especially in immunocompromised patients. Combination therapy of amikacin and imipenem is commonly used to treat severe nocardial infections. We describe a patient with imipenem-resistant Nocardia cyriacigeorgica, which, to our knowledge, has not been previously reported among isolates of this species.

Species that belong to the Nocardia genus are filamentous strict aerobic Gram-positive bacteria. The traditional identification system of these species is based on the phenotypic, biochemical and chemotaxonomic characteristics. However, new methods based on the study of 16S ribosomal RNA have allowed a remarkable increase in the detection of new species. This is considered an important identification tool, it is also a less time consuming process. This study shows 53 strains of clinical origin, the DNA was extracted and amplified from pure colonies growing on Bennett's agar. A PCR was conducted using primers Nod and Noc2 (Rodriguez-Nava et al., 2006) [23], which enabled us to amplify a specific region of 16S rRNA, followed by sequencing each of the PCR products. This approach allowed us to identify molecular species frequently reported as etiological agents of actinomycetoma and nocardiosis, such as N. brasiliensis, N. otitidiscaviarum, N. farcinica, and N. nova, as well as other species that have been described recently as N. cerradoensis, N. mexicana, N. cyriacigeorgica, and N. veterana, which so far have not been reported in clinical cases in Venezuela. (C) 2011 Elsevier Masson SAS. All rights reserved.

We report a case of cavitary pneumonia caused by N. otitidiscaviarum in a man with diabetes mellitus and thrombocytopenia treated with systemic corticosteroid. Taxonomic identification involved phenotypic testing and molecular identification that was carried out by DNA sequencing of the 16SrRNA gene.

ABSTRACT Nocardia takedensis is a recently described species isolated from soil. The first clinical isolate in Japan has recently been reported. This report describes the first clinical isolate of N. takedensis in Spain from a respiratory specimen.